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- PDB-3dkn: Sec61 in the Canine ribosome-channel complex from the endoplasmic... -

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Basic information

Entry
Database: PDB / ID: 3dkn
TitleSec61 in the Canine ribosome-channel complex from the endoplasmic reticulum
Components
  • (Preprotein translocase subunit ...) x 3
  • RNA (32-MER)
  • RNA (5'-R(P*AP*GP*CP*CP*GP*CP*AP*CP*GP*GP*AP*GP*GP*CP*GP*AP*A)-3')
  • RNA (5'-R(P*CP*GP*UP*GP*CP*CP*AP*AP*GP*CP*UP*GP*CP*GP*AP*UP*AP*AP*GP*C)-3')
Keywordsprotein transport/RNA / Ribosome-channel complex / co-translational translocation / endoplasmic reticulum / protein transport-RNA COMPLEX
Function / homology
Function and homology information


intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / protein transport / plasma membrane
Similarity search - Function
Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. ...Preprotein translocase subunit SecG / Protein translocase subunit SecY / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY
Similarity search - Domain/homology
RNA / RNA (> 10) / Preprotein translocase subunit SecG / Protein translocase subunit SecE / Protein translocase subunit SecY
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsMenetret, J.-F. / Akey, C.
CitationJournal: Structure / Year: 2008
Title: Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome.
Authors: Jean-François Ménétret / Ramanujan S Hegde / Mike Aguiar / Steven P Gygi / Eunyong Park / Tom A Rapoport / Christopher W Akey /
Abstract: During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we ...During cotranslational protein translocation, the ribosome associates with a membrane channel, formed by the Sec61 complex, and recruits the translocon-associated protein complex (TRAP). Here we report the structure of a ribosome-channel complex from mammalian endoplasmic reticulum in which the channel has been visualized at 11 A resolution. In this complex, single copies of Sec61 and TRAP associate with a nontranslating ribosome and this stoichiometry was verified by quantitative mass spectrometry. A bilayer-like density surrounds the channel and can be attributed to lipid and detergent. The crystal structure of an archaeal homolog of the Sec61 complex was then docked into the map. In this model, two cytoplasmic loops of Sec61 may interact with RNA helices H6, H7, and H50, while the central pore is located below the ribosome tunnel exit. Hence, this copy of Sec61 is positioned to capture and translocate the nascent chain. Finally, we show that mammalian and bacterial ribosome-channel complexes have similar architectures.
History
DepositionJun 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Simplified surface model + fitted atomic model
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
D: RNA (5'-R(P*CP*GP*UP*GP*CP*CP*AP*AP*GP*CP*UP*GP*CP*GP*AP*UP*AP*AP*GP*C)-3')
E: RNA (5'-R(P*AP*GP*CP*CP*GP*CP*AP*CP*GP*GP*AP*GP*GP*CP*GP*AP*A)-3')
F: RNA (32-MER)
A: Preprotein translocase subunit secY
B: Preprotein translocase subunit secE
C: Preprotein translocase subunit secG


Theoretical massNumber of molelcules
Total (without water)80,0726
Polymers80,0726
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules DEF

#1: RNA chain RNA (5'-R(P*CP*GP*UP*GP*CP*CP*AP*AP*GP*CP*UP*GP*CP*GP*AP*UP*AP*AP*GP*C)-3')


Mass: 6421.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: helix 6 / Source: (natural) Canis lupus familiaris (dog)
#2: RNA chain RNA (5'-R(P*AP*GP*CP*CP*GP*CP*AP*CP*GP*GP*AP*GP*GP*CP*GP*AP*A)-3')


Mass: 5543.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: helix 7 / Source: (natural) Canis lupus familiaris (dog)
#3: RNA chain RNA (32-MER)


Mass: 10289.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: helix 50 / Source: (natural) Canis lupus familiaris (dog)

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Preprotein translocase subunit ... , 3 types, 3 molecules ABC

#4: Protein Preprotein translocase subunit secY / Protein transport protein SEC61 subunit alpha homolog


Mass: 46736.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q60175*PLUS
#5: Protein Preprotein translocase subunit secE / Protein transport protein Sec61 gamma subunit homolog


Mass: 7440.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: Q57817*PLUS
#6: Protein/peptide Preprotein translocase subunit secG / Protein transport protein Sec61 subunit beta homolog


Mass: 3639.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / References: UniProt: P60460*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent-ID
1Ribosome-channel complexesRIBOSOME0
2Sec61 channel1
3large subunitProtein subunit1
Buffer solutionName: 30mM Hepes 50mM KAc, 10mM Mg acetate and 1.5% digitonin.
pH: 7.5
Details: 30mM Hepes 50mM KAc, 10mM Mg acetate and 1.5% digitonin.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: continuous thin carbon on 400 mesh copper grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Home-made plunger

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jul 27, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 51000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2 mm
Specimen holderTemperature: 93 K
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3EMAN3D reconstruction
CTF correctionDetails: per micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: projection matching with EMAN / Resolution: 8.7 Å / Num. of particles: 79000 / Actual pixel size: 2.73 Å / Magnification calibration: vermiculite crystals
Details: 8.7 angstrom resolution for the 80S ribosome, 11.1 angstrom resolution for the Sec61 region of the channel density
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--Rigid body, then local flexible fitting
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11RHZ11RHZ1PDBexperimental model
21S7211S722PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 1482 0 0 5554

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